def test_property_domain(self):
rdf_content = rdf_prefix + '''
:Entity a owl:Class .
:Type a owl:Class .
:Place a owl:Class .
:Other a owl:Class ;
:common_properties :code .
:code a owl:DatatypeProperty ;
rdfs:domain [
a owl:Class ;
owl:unionOf (
:Type
:Place
)
] ;
schema:domainIncludes :Entity .
'''
ontology = Ontology(rdf_content)
property_code = ontology.get_entity(DIG.code.toPython())
self.assertIsInstance(property_code, OntologyDatatypeProperty)
self.assertEqual(len(property_code.included_domains()), 4)
self.assertSetEqual(
property_code.included_domains(),
set(
map(ontology.get_entity,
map(str, (DIG.Entity, DIG.Type, DIG.Other, DIG.Place)))))
def test_property_merge_config_closest_inherit(self):
rdf_content = rdf_prefix + '''
:had_participant a owl:ObjectProperty ; .
:carried_out_by a owl:ObjectProperty ;
owl:subPropertyOf :had_participant ; .
:custody_received_by a owl:ObjectProperty ;
owl:subPropertyOf :carried_out_by ; .
'''
ontology = Ontology(rdf_content)
config = ontology.merge_with_master_config(
'{"fields":{"had_participant":{"color":"red"},'
'"carried_out_by":{"color":"blue"}}}')
self.assertTrue('fields' in config)
fields = config['fields']
self.assertIn('had_participant', fields)
property_ = fields['had_participant']
self.assertIn('color', property_)
self.assertEqual('red', property_['color'])
self.assertIn('carried_out_by', fields)
sub_property = fields['carried_out_by']
self.assertIn('color', sub_property)
self.assertEqual('blue', sub_property['color'])
self.assertIn('custody_received_by', fields)
subsub = fields['custody_received_by']
self.assertIn('color', subsub)
self.assertEqual(sub_property['color'], subsub['color'])
def setUp(self):
ontology_content = '''
@prefix : <http://dig.isi.edu/ontologies/dig/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix schema: <http://schema.org/> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
:Person a owl:Class ;
rdfs:subClassOf :Actor, :Biological_Object ;
:common_properties :label, :title, :religion ; .
:has_name a owl:DatatypeProperty ;
schema:domainIncludes :Person ;
schema:rangeIncludes xsd:string ; .
:has_child a owl:ObjectProperty ;
schema:domainIncludes :Person ;
schema:rangeIncludes :Person ; .
'''
ontology = Ontology(ontology_content,
validation=False,
include_undefined_class=True,
quiet=True)
kg_schema = KGSchema(ontology.merge_with_master_config(dict()))
etk = ETK(kg_schema=kg_schema,
ontology=ontology,
generate_json_ld=True)
etk2 = ETK(kg_schema=kg_schema,
ontology=ontology,
generate_json_ld=False)
self.doc = etk.create_document(dict(),
doc_id='http://xxx/1',
type_=[DIG.Person.toPython()])
self.doc2 = etk2.create_document(dict(),
doc_id='http://xxx/2',
type_=[DIG.Person.toPython()])
def test_property_merge_master_config(self):
rdf_content = rdf_prefix + ':had_participant a owl:ObjectProperty . '
ontology = Ontology(rdf_content)
d_color = 'red'
config = ontology.merge_with_master_config('{}', {'color': d_color})
self.assertIn('fields', config)
fields = config['fields']
self.assertIn('had_participant', fields)
property_ = fields['had_participant']
self.assertIn('color', property_)
self.assertEqual(property_['color'], d_color)
def test_inverse_object_property(self):
rdf_content = rdf_prefix + '''
:moved_to a owl:ObjectProperty ;
:inverse :was_destination_of .
'''
ontology = Ontology(rdf_content)
self.assertEqual(len(ontology.all_properties()), 2)
property_moved = ontology.get_entity(DIG.moved_to.toPython())
property_inverse = ontology.get_entity(DIG.was_destination_of.toPython())
self.assertIsNotNone(property_moved)
self.assertIsNotNone(property_inverse)
self.assertTrue(property_moved.is_primary())
self.assertFalse(property_inverse.is_primary())
self.assertEqual(property_moved.inverse(), property_inverse)
self.assertEqual(property_inverse.inverse(), property_moved)
def test_ontology_api_is_valid_with_empty_kg(self):
import json
rdf_content = rdf_prefix + '''
:Place a owl:Class ;
:common_properties :region ; .
:region a owl:DatatypeProperty ;
schema:domainIncludes :Place ;
schema:rangeIncludes xsd:string ; .
'''
kg = '{}'
ontology = Ontology(rdf_content)
self.assertTrue(ontology.is_valid('region', 'somewhere', json.loads(kg)))
self.assertFalse(ontology.is_valid('region', 1, json.loads(kg)))
self.assertFalse(ontology.is_valid('region', True, json.loads(kg)))
def test_property_merge_config_delete_orphan(self):
rdf_content = rdf_prefix + '''
:had_participant a owl:ObjectProperty ; .
:carried_out_by a owl:ObjectProperty ;
owl:subPropertyOf :had_participant ; .
'''
ontology = Ontology(rdf_content)
config = ontology.merge_with_master_config('{"fields":{"had_participant":{"color":"red"},'
'"custody_received_by":{"color":"blue"}}}',
delete_orphan_fields=True)
self.assertTrue('fields' in config)
fields = config['fields']
self.assertIn('had_participant', fields)
self.assertIn('carried_out_by', fields)
self.assertNotIn('custody_received_by', fields)
def test_property_range_inherit_consistency(self):
rdf_content = rdf_prefix + '''
:Event a owl:Class ; .
:Entity a owl:Class ;
.
:Group a owl:Class ;
rdfs:subClassOf :Entity ;
.
:Actor a owl:Class ;
rdfs:subClassOf :Group ;
.
:Physical_Object a owl:Class ;
rdfs:subClassOf :Entity ;
.
:Man_Made_Thing a owl:Class ;
rdfs:subClassOf :Entity ;
.
:had_participant a owl:ObjectProperty ;
schema:rangeIncludes :Actor ;
.
:transferred_custody_of a owl:ObjectProperty ;
schema:rangeIncludes :Physical_Object, :Man_Made_Thing ;
owl:subPropertyOf :had_participant ;
.
'''
with self.assertRaises(ValidationError):
Ontology(rdf_content)
def test_class_cycle_detection(self):
rdf_content = rdf_prefix + '''
:Entity a owl:Class ;
rdfs:label "Entity" ;
skos:definition """Everything that can be described, similar to owl:Thing.""" ;
owl:subClassOf :Actor ;
:common_properties :label, :title, :description ;
:crm_equivalent crm:E1_CRM_Entity
.
:Group a owl:Class ;
rdfs:label "Group" ;
skos:definition """A """ ;
rdfs:subClassOf :Entity ;
:crm_equivalent crm:E74_Group ;
:common_properties :label, :title ;
.
:Actor a owl:Class ;
rdfs:label "Actor" ;
skos:definition """A group, organization, person who have the potential to do actions.""" ;
rdfs:subClassOf :Group ;
:crm_equivalent crm:E39_Actor ;
:common_properties :label, :title, :religion ;
.
'''
with self.assertRaises(ValidationError):
Ontology(rdf_content)
def test_datatype_property_range(self):
rdf_content = rdf_prefix + '''
:code a owl:DatatypeProperty ;
schema:rangeIncludes xsd:string ;
.
:iso_code a owl:DatatypeProperty ;
rdfs:subPropertyOf :code ;
.
'''
ontology = Ontology(rdf_content)
property_code = ontology.get_entity(DIG.code.toPython())
property_iso_code = ontology.get_entity(DIG.code.toPython())
self.assertIsInstance(property_iso_code, OntologyDatatypeProperty)
self.assertTrue(property_code.is_legal_object(XSD.string.toPython()))
self.assertTrue(property_iso_code.is_legal_object(XSD.string.toPython()))
self.assertFalse(property_code.is_legal_object(XSD.dateTime.toPython()))
self.assertFalse(property_iso_code.is_legal_object(XSD.dateTime.toPython()))
def __init__(self, ontology: Ontology):
self.ontology = ontology
self.classes = ontology.classes
self.properties = ontology.all_properties()
self.data_properties = ontology.data_properties
self.object_properties = ontology.object_properties
self.item = '<h4 id="{}">{}</h4>\n<div class="entity">\n<table>\n{}\n</table>\n</div>'
self.row = '<tr>\n<th align="right" valign="top">{}</th>\n<td>{}</td>\n</tr>'
def test_property_hierachy(self):
rdf_content = rdf_prefix + '''
:code a owl:DatatypeProperty ; .
:iso_code a owl:DatatypeProperty ;
rdfs:subPropertyOf :code ; .
:cameo_code a owl:DatatypeProperty ;
rdfs:subPropertyOf :code ; .
:iso_country_code a owl:DatatypeProperty ;
rdfs:subPropertyOf :iso_code ; .
:adm1_code a owl:DatatypeProperty ;
rdfs:subPropertyOf :iso_code ; .
'''
ontology = Ontology(rdf_content)
self.assertEqual(len(ontology.all_classes()), 0)
self.assertEqual(len(ontology.all_properties()), 5)
code = ontology.get_entity(DIG.code.toPython())
self.assertIsNotNone(code)
self.assertIsInstance(code, OntologyDatatypeProperty)
iso_code = ontology.get_entity(DIG.iso_code.toPython())
self.assertIsNotNone(iso_code)
iso_country_code = ontology.get_entity(DIG.iso_country_code.toPython())
self.assertIsNotNone(iso_country_code)
self.assertSetEqual(iso_code.super_properties(), {code})
self.assertSetEqual(iso_country_code.super_properties_closure(),
{code, iso_code})
def test_property_merge_config_inherit(self):
rdf_content = rdf_prefix + '''
:had_participant a owl:ObjectProperty ; .
:transferred_custody_of a owl:ObjectProperty ;
owl:subPropertyOf :had_participant ; .
'''
ontology = Ontology(rdf_content)
config = ontology.merge_with_master_config('{"fields":{"had_participant":{"color":"red"}}}')
self.assertIn('fields', config)
fields = config['fields']
self.assertIn('had_participant', fields)
property_ = fields['had_participant']
self.assertIn('color', property_)
self.assertEqual(property_['color'], 'red')
self.assertIn('transferred_custody_of', fields)
sub_property = fields['transferred_custody_of']
self.assertIn('color', sub_property)
self.assertEqual(property_['color'], sub_property['color'])
def test_ontology_api_is_valid_with_kg(self):
import json
rdf_content = rdf_prefix + '''
:Human a owl:Class ; .
:Place a owl:Class ;
:common_properties :region ; .
:region a owl:DatatypeProperty ;
schema:domainIncludes :Place ;
schema:rangeIncludes xsd:string ; .
'''
kg = '''
{
"@type": ["dig:Place"],
"@id": "some_doc_id",
"@context": {
"dig": "http://dig.isi.edu/ontologies/dig/"
}
}
'''
kg_wrong_domain = '''
{
"@type": ["dig:Human"],
"@id": "some_doc_id",
"@context": {
"dig": "http://dig.isi.edu/ontologies/dig/"
}
}
'''
kg_domain_doesnt_exist = '''
{
"@type": ["dig:People"],
"@id": "some_doc_id",
"@context": {
"dig": "http://dig.isi.edu/ontologies/dig/"
}
}
'''
ontology = Ontology(rdf_content)
self.assertTrue(ontology.is_valid('region', 'somewhere', json.loads(kg)))
self.assertFalse(ontology.is_valid('region', 'somewhere', json.loads(kg_wrong_domain)))
self.assertFalse(ontology.is_valid('region', 'somewhere', json.loads(kg_domain_doesnt_exist)))
def test_ontology_schema_org_datatype(self):
import json
rdf_content = rdf_prefix + '''
schema:Person a owl:Class ; .
schema:Text a schema:DataType, rdfs:Class ; .
schema:name
a rdf:Property ;
schema:domainIncludes schema:Person ;
schema:rangeIncludes schema:Person .
'''
kg = '''
{
"@type": ["http://schema.org/Person"],
"@id": "person1",
"http://schema.org/name": "Person Name"
}
'''
ontology = Ontology(rdf_content)
for entity in ontology.all_classes():
self.assertIsInstance(entity, OntologyEntity)
self.assertIsInstance(entity, OntologyClass)
self.assertEqual(len(ontology.all_properties()), 1)
return_value = ontology.is_valid('schema:name',
"person name1",
json.loads(kg))
self.assertEqual(return_value, {'@id': 'person name1'})
rdf_content = rdf_prefix + '''
schema:Person a owl:Class ; .
schema:DataType a owl:Class ; .
schema:Text a schema:DataType, owl:Class ; .
schema:name
a rdf:Property ;
schema:domainIncludes schema:Person ;
schema:rangeIncludes schema:Text .
'''
ontology = Ontology(rdf_content)
kg = '''
{
"@type": ["http://schema.org/Person"],
"@id": "person1",
"http://schema.org/name": "Person Name"
}
'''
return_value = ontology.is_valid('schema:name',
"person name1",
json.loads(kg))
self.assertEqual(return_value, {'@value': 'person name1'})
def run(args):
contents = [open(f).read() for f in args.files]
ontology = Ontology(contents,
validation=args.validation,
include_undefined_class=args.include_class,
quiet=args.quiet)
doc_content = OntologyReportGenerator(ontology).generate_html_report(
include_turtle=args.include_turtle,
exclude_warning=args.exclude_warning,
list_auxiliary_line=args.list_auxiliary)
with open(args.out, "w") as f:
f.write(doc_content)
def test_ontology_condensed_json(self):
import json
rdf_content = rdf_prefix + '''
schema:Person a owl:Class ; .
schema:DataType a owl:Class ; .
schema:Text a schema:DataType, owl:Class ; .
schema:name
a rdf:Property ;
schema:domainIncludes schema:Person ;
schema:rangeIncludes schema:Text .
'''
ontology = Ontology(rdf_content, expanded_jsonld=False)
kg = '''
{
"@type": ["http://schema.org/Person"],
"@id": "person1",
"http://schema.org/name": "Person Name"
}
'''
return_value = ontology.is_valid('schema:name', "person name1",
json.loads(kg))
self.assertEqual(return_value, 'person name1')
def test_property_class_consistency(self):
rdf_content = rdf_prefix + '''
:Entity a owl:Class ; .
:Place a owl:Class ; .
:code a owl:DatatypeProperty ;
schema:domainIncludes :Entity ;
schema:rangeIncludes xsd:string ; .
:country a owl:ObjectProperty ;
rdfs:subPropertyOf :code ;
schema:domainIncludes :Place ;
schema:rangeIncludes :Country ; .
'''
with self.assertRaises(ValidationError):
Ontology(rdf_content)
def test_property_domain_inherit_redundant(self):
rdf_content = rdf_prefix + '''
:Event a owl:Class ; .
:had_participant a owl:ObjectProperty ;
schema:domainIncludes :Event ;
.
:transferred_ownership_to a owl:ObjectProperty ;
schema:domainIncludes :Event ;
owl:subPropertyOf :carried_out_by ;
.
:carried_out_by a owl:ObjectProperty ;
owl:subPropertyOf :had_participant ;
.
'''
with self.assertLogs(level="WARNING"):
Ontology(rdf_content)
def test_property_domain_inherit_consistency(self):
rdf_content = rdf_prefix + '''
:Thing a owl:Class ; .
:Event a owl:Class ;
rdfs:subClassOf :Thing ; .
:had_participant a owl:ObjectProperty ;
schema:domainIncludes :Event ; .
:transferred_ownership_to a owl:ObjectProperty ;
schema:domainIncludes :Thing ;
owl:subPropertyOf :carried_out_by ; .
:carried_out_by a owl:ObjectProperty ;
owl:subPropertyOf :had_participant ; .
'''
with self.assertRaises(ValidationError):
Ontology(rdf_content)
def test_basic_entity_info(self):
rdf_content = rdf_prefix + '''
:Entity a owl:Class ;
rdfs:label "Entity" ;
skos:definition """Everything that can be described, similar to owl:Thing.""" ;
:common_properties :label, :title, :description ;
.
'''
ontology = Ontology(rdf_content)
self.assertEqual(len(ontology.all_classes()), 1)
for entity in ontology.all_classes():
self.assertIsInstance(entity, OntologyEntity)
self.assertIsInstance(entity, OntologyClass)
self.assertEqual(len(ontology.all_properties()), 0)
for entity in ontology.all_properties():
self.assertIsInstance(entity, OntologyEntity)
self.assertIsInstance(entity, OntologyProperty)
self.assertEqual(len(ontology.root_classes()), 1)
for entity in ontology.root_classes():
self.assertIsInstance(entity, OntologyClass)
self.assertEqual(len(entity.super_classes()), 0)
def test_property_cycle_detection(self):
rdf_content = rdf_prefix + '''
:Entity a owl:Class ; .
:code a owl:DatatypeProperty ;
rdfs:label "code" ;
skos:definition """A short string used as a code for an entity.""" ;
skos:note """Examples are country codes, currency codes.""" ;
schema:domainIncludes :Entity ;
schema:rangeIncludes xsd:string ;
rdfs:subPropertyOf :iso_code ;
.
:iso_code a owl:DatatypeProperty ;
rdfs:label "ISO code" ;
skos:definition """A sanctioned ISO code for something.""" ;
rdfs:subPropertyOf :code ;
.
'''
with self.assertRaises(ValidationError):
Ontology(rdf_content)
def test_class_hierachy(self):
rdf_content = rdf_prefix + '''
:Entity a owl:Class ; .
:Group a owl:Class ;
rdfs:subClassOf :Entity ; .
:Actor a owl:Class ;
owl:subClassOf :Group ; .
'''
ontology = Ontology(rdf_content)
self.assertEqual(len(ontology.all_classes()), 3)
entity = ontology.get_entity(DIG.Entity.toPython())
self.assertIsNotNone(entity)
self.assertSetEqual(ontology.root_classes(), {entity})
group = ontology.get_entity(DIG.Group.toPython())
self.assertIsNotNone(group)
actor = ontology.get_entity(DIG.Actor.toPython())
self.assertIsNotNone(actor)
self.assertSetEqual(group.super_classes(), {entity})
self.assertSetEqual(actor.super_classes(), {group})
self.assertSetEqual(actor.super_classes_closure(), {entity, group})
def test_ontology_schema_org(self):
import json
rdf_content = rdf_prefix + '''
schema:Person a owl:Class ; .
schema:relatedTo
a rdf:Property ;
schema:domainIncludes schema:Person ;
schema:rangeIncludes schema:Person .
'''
kg = '''
{
"@type": ["http://schema.org/Person"],
"@id": "person1",
"http://schema.org/relatedTo": {
"@type": ["http://schema.org/Person"],
"@id": "person2"
}
}
'''
ontology = Ontology(rdf_content)
for entity in ontology.all_classes():
self.assertIsInstance(entity, OntologyEntity)
self.assertIsInstance(entity, OntologyClass)
self.assertEqual(len(ontology.all_properties()), 1)
kg_json = json.loads(kg)
config = ontology.merge_with_master_config(kg_json,
delete_orphan_fields=True)
self.assertTrue('fields' in config)
fields = config['fields']
self.assertIn('relatedTo', fields)
#
self.assertTrue(
ontology.is_valid('schema:relatedTo',
kg_json["http://schema.org/relatedTo"], kg_json))
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix schema: <http://schema.org/> .
:Event a owl:Class ; .
:Entity a owl:Class ; .
:Organization a owl:Class ; .
:MOVEMENT_TRANSPORT a owl:Class ; .
:GeopoliticalEntity a owl:Class ; .
skos:prefLabel a owl:DatatypeProperty ;
schema:domainIncludes :Entity, :Event ;
rdfs:range xsd:string ; .
:conflict_attack_place a owl:ObjectProperty ;
schema:domainIncludes :Entity, :Event ;
schema:rangeIncludes :GeopoliticalEntity ; .
'''
ontology = Ontology(ontology_content,
validation=False,
include_undefined_class=True,
quiet=True)
kg_schema = KGSchema(ontology.merge_with_master_config(dict()))
etk = ETK(modules=ExampleETKModule, kg_schema=kg_schema, ontology=ontology)
input_data = {'doc_id': '1', 'data': json.loads(sample_input)}
doc = etk.create_document(input_data)
docs = etk.process_ems(doc)
kgs = [json.dumps(doc.kg.value) for doc in docs[1:]]
with open('output.jsonl', 'w') as f:
f.write('\n'.join(kgs))
with open('output.nt', 'w') as f:
f.writelines(map(rdf_generation, kgs))
import sys, os
sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
sys.path.append(os.path.join(os.path.dirname(__file__), '../..'))
from etk.ontology_api import Ontology
from etk.ontology_report_generator import OntologyReportGenerator
dir_path = os.path.dirname(os.path.abspath(__file__))
input_turtle = dir_path + "/../../ontologies/default-ontology.ttl"
output_doc = dir_path + "/default-ontology.html"
doc_content = ""
with open(input_turtle) as f:
ontology = Ontology(f.read(),
validation=False,
include_undefined_class=True)
doc_content = OntologyReportGenerator(ontology).generate_html_report(
include_turtle=True)
with open(output_doc, "w") as f:
f.write(doc_content)
